After solving another mystery they weren't welcome to, Fred, Daphne, Velma, Shaggy, and his dog, Scooby-Doo are warned off by the Sheriff because their town's strange and spooky mysteries have turned it into a tourist attraction; and their parents each think the other kid is a bad influencing on their own. But when a slime mutant caccoons it's victims, these kids aren't going to sit idly by while there's another mystery to solve whether the townsfolk like it or not.

The Hex Girls are in town to perform a concert, but bring along a phantom who is attempting to keep them from playing. Meanwhile, Scooby-Doo is still angry at Shaggy for going to the prom with Velma, so he makes a new best friend, a dummy called Harry.

An evil Gnome doesn't take kindly to people dressed as pirates at Crystal Cove's renaissance fair; Velma is annoyed at Shaggy for him not paying enough attention to her because of his close bond with Scooby.

Two giant monsters, named Humungonauts, are attacking Crystal Cove; once again Mr. E intervenes to help the gang solve the mystery. Meanwhile, Scooby stumbles across Velma and Shaggy kissing, and discovers their relationship, and Shaggy is forced to decide who he would rather be with. Fred decides that the gang should have a name, "Mystery Incorporated", in honor of those that came before them. Unfortunately he also decides that the gang should start wearing team uniforms.

Employees of Destroido are being attacked by a Cicada Creature which can command swarms of the insects. Meanwhile, Daphne's infatuation over Dr. Yantz gets Fred enough to make him to finally ask her out, but traps and dates don't go over so well.